1 Plan

Repeat comparison but include bombyx.

Compare to d melanogaster. then also comapre across in both directiosns.

Look for overlaps.

require(magrittr)
## Loading required package: magrittr
require(tidyverse)
## Loading required package: tidyverse
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
## ✔ ggplot2 3.3.2     ✔ purrr   0.3.4
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## ✔ tidyr   1.1.2     ✔ stringr 1.4.0
## ✔ readr   1.4.0     ✔ forcats 0.5.0
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
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## ✖ dplyr::filter()    masks stats::filter()
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require(ShortRead)
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require(Herper)
## Loading required package: Herper
## Loading required package: reticulate
file.copy("/rugpfs/fs0/brc/scratch/tcarroll/autoProcessing/BRC/obiroi/obiroi.fa", "obiroi.fa")
o_fa<-readFasta("obiroi.fa")

require(Herper)
export_CondaEnv("eggnog", yml_export= "eggnog_tom.yml", file.path("/rugpfs/fs0/brc/scratch/tcarroll/autoProcessing/","eggnogConda"))
import_CondaEnv("eggnog_tom.yml", "eggnog", pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda")

#install_CondaTools("ete3_external_apps","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper/eggnog",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)
#external apps is not installed. this gives warning in build check. unclear why or if needed. 

Herper::with_CondaEnv("eggnog",system("ete3 build check"),pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda")
Herper::with_CondaEnv("eggnog",system("ete3 ncbiquery -v 0"),pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda")


#install_CondaTools("python=2.7","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)

#install_CondaTools("ete3_external_apps","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)

# install_CondaTools(c("eggnog-mapper","ete3","ete_toolchain","ete3_external_apps"),"eggnog",channels="etetoolkit", pathToMiniConda= "/rugpfs/fs0/brc/scratch/mpaul/herper_conda/")
# install_CondaTools("ete3","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)
# install_CondaTools("ete_toolchain","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper_conda",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)
#install_CondaTools("ete3_external_apps","eggnog",pathToMiniConda="/rugpfs/fs0/brc/scratch/mpaul/herper/eggnog",updateEnv=TRUE,channels="etetoolkit",verbose=TRUE)
read.delim("TC_ 20201201_Result/eggnogAnno_CondaVersionPy2_Scopeis50557_Targetis7227.emapper.annotations", skip = 3) %>% DT::datatable()
## Warning in instance$preRenderHook(instance): It seems your data is too big
## for client-side DataTables. You may consider server-side processing: https://
## rstudio.github.io/DT/server.html
read.delim("TC_ 20201201_Result/eggnogAnno_WithPredictOrthp_CondaVersionPy2.emapper.predict_orthologs", skip = 3) %>% DT::datatable()
test <- read.delim("TC_ 20201201_Result/eggnogAnno_WithPredictOrthp_CondaVersionPy2.emapper.predict_orthologs")
nrow(test)
## [1] 727
# seed_ortholog just shows first 4 columns of the annotations result
# read.delim("TC_ 20201201_Result/eggnogAnno_CondaVersionPy2_Scopeis50557_Targetis7227.emapper.seed_orthologs", skip = 5) %>% DT::datatable()


#We are missing the orhtolog file 
Herper::with_CondaEnv("eggnog",system("python /rugpfs/fs0/brc/scratch/mpaul/eggnog/refactor-old/emapper.py -i /rugpfs/fs0/brc/scratch/tcarroll/autoProcessing/BRC/obiroi/obiroi.fa --cpu 30 -m diamond --tax_scope 50557 --target_taxa 7227 --resume --data_dir /rugpfs/fs0/brc/scratch/tcarroll/autoProcessing//eggnogConda/dataDirConda/ --output  /rugpfs/fs0/brc/scratch/mpaul/1_kronauer/orli/Kronauer_Orli/20201201_OS_eggnog/eggnogAnno_refactor_Scopeis50557_Targetis7227"),pathToMiniConda=file.path("/rugpfs/fs0/brc/scratch/tcarroll/autoProcessing/","eggnogConda"))
list_CondaPkgs("eggnog",pathToMiniConda=file.path("/rugpfs/fs0/brc/scratch/tcarroll/autoProcessing/","eggnogConda"))
##                name          version     channel platform
## 1     _libgcc_mutex              0.1   pkgs/main linux-64
## 2         argtable2             2.13  etetoolkit linux-64
## 3         biopython             1.68    bioconda linux-64
## 4              blas              1.0   pkgs/main linux-64
## 5             boost           1.67.0   pkgs/main linux-64
## 6             bzip2            1.0.8   pkgs/main linux-64
## 7   ca-certificates       2020.10.14   pkgs/main linux-64
## 8           certifi        2020.6.20   pkgs/main   noarch
## 9          clustalo            1.2.4  etetoolkit linux-64
## 10             dbus          1.13.18   pkgs/main linux-64
## 11        dialigntx            1.0.2  etetoolkit linux-64
## 12          diamond           0.9.24    bioconda linux-64
## 13    eggnog-mapper            2.0.1    bioconda   noarch
## 14             ete3            3.1.2  etetoolkit   noarch
## 15    ete_toolchain            3.0.0  etetoolkit linux-64
## 16            expat           2.2.10   pkgs/main linux-64
## 17         fasttree              2.1  etetoolkit linux-64
## 18       fontconfig           2.13.0   pkgs/main linux-64
## 19         freetype           2.10.4   pkgs/main linux-64
## 20             glib           2.66.1   pkgs/main linux-64
## 21 gst-plugins-base           1.14.0   pkgs/main linux-64
## 22        gstreamer           1.14.0   pkgs/main linux-64
## 23              icu             58.2   pkgs/main linux-64
## 24     intel-openmp           2020.2   pkgs/main linux-64
## 25           iqtree            1.5.5  etetoolkit linux-64
## 26             jpeg               9b   pkgs/main linux-64
## 27           kalign             2.03  etetoolkit linux-64
## 28          libblas            3.8.0 conda-forge linux-64
## 29         libboost           1.67.0   pkgs/main linux-64
## 30         libcblas            3.8.0 conda-forge linux-64
## 31          libedit     3.1.20191231   pkgs/main linux-64
## 32           libffi              3.3   pkgs/main linux-64
## 33           libgcc            7.2.0   pkgs/main linux-64
## 34        libgcc-ng            9.1.0   pkgs/main linux-64
## 35   libgfortran-ng            7.3.0   pkgs/main linux-64
## 36        liblapack            3.8.0 conda-forge linux-64
## 37           libpng           1.6.37   pkgs/main linux-64
## 38     libstdcxx-ng            9.1.0   pkgs/main linux-64
## 39          libtiff            4.1.0   pkgs/main linux-64
## 40          libuuid            1.0.3   pkgs/main linux-64
## 41           libxcb             1.14   pkgs/main linux-64
## 42          libxml2           2.9.10   pkgs/main linux-64
## 43          libxslt           1.1.34   pkgs/main linux-64
## 44             lxml            3.8.0 conda-forge linux-64
## 45            lz4-c            1.9.2   pkgs/main linux-64
## 46            mafft            6.861  etetoolkit linux-64
## 47              mkl           2020.2   pkgs/main linux-64
## 48      mkl-service            2.3.0   pkgs/main linux-64
## 49          mkl_fft           1.0.15   pkgs/main linux-64
## 50       mkl_random            1.1.0   pkgs/main linux-64
## 51      mmtf-python            1.0.2    bioconda linux-64
## 52   msgpack-python            0.6.1   pkgs/main linux-64
## 53           muscle           3.8.31  etetoolkit linux-64
## 54          ncurses              6.2   pkgs/main linux-64
## 55            numpy           1.16.6   pkgs/main linux-64
## 56       numpy-base           1.16.6   pkgs/main linux-64
## 57          olefile             0.46   pkgs/main linux-64
## 58          openssl           1.1.1h   pkgs/main linux-64
## 59             paml              4.8  etetoolkit linux-64
## 60             pcre             8.44   pkgs/main linux-64
## 61       phylobayes             4.1c  etetoolkit linux-64
## 62            phyml 20160115.patched  etetoolkit linux-64
## 63           pillow            6.2.1   pkgs/main linux-64
## 64              pip           19.3.1   pkgs/main linux-64
## 65       pmodeltest              1.4  etetoolkit linux-64
## 66         py-boost           1.67.0   pkgs/main linux-64
## 67             pyqt            5.9.2   pkgs/main linux-64
## 68           python           2.7.18   pkgs/main linux-64
## 69               qt            5.9.7   pkgs/main linux-64
## 70            raxml           8.2.11  etetoolkit linux-64
## 71         readline              8.0   pkgs/main linux-64
## 72        reportlab           3.5.26   pkgs/main linux-64
## 73            scipy            1.2.1 conda-forge linux-64
## 74       setuptools           44.0.0   pkgs/main linux-64
## 75              sip           4.19.8   pkgs/main linux-64
## 76              six           1.15.0   pkgs/main   noarch
## 77              slr            1.4.3  etetoolkit linux-64
## 78           sqlite           3.33.0   pkgs/main linux-64
## 79         t_coffee            11.00  etetoolkit linux-64
## 80               tk           8.6.10   pkgs/main linux-64
## 81           trimal              1.4  etetoolkit linux-64
## 82             wget           1.20.1   pkgs/main linux-64
## 83            wheel           0.35.1   pkgs/main   noarch
## 84               xz            5.2.5   pkgs/main linux-64
## 85             zlib           1.2.11   pkgs/main linux-64
## 86             zstd            1.4.5   pkgs/main linux-64
devtools::session_info()
## Warning in system("timedatectl", intern = TRUE): running command 'timedatectl'
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##  setting  value                                      
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##  os       Red Hat Enterprise Linux Server 7.5 (Maipo)
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##  tz       America/New_York                           
##  date     2020-12-04                                 
## 
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##  assertthat             0.2.1    2019-03-21 [1]
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##  Biobase              * 2.48.0   2020-04-27 [1]
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##  generics               0.1.0    2020-10-31 [1]
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##  GenomicAlignments    * 1.24.0   2020-04-27 [1]
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##  magrittr             * 1.5      2014-11-22 [1]
##  Matrix                 1.2-18   2019-11-27 [1]
##  matrixStats          * 0.57.0   2020-09-25 [1]
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##  rprojroot              1.3-2    2018-01-03 [1]
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##  sessioninfo            1.1.1    2018-11-05 [1]
##  ShortRead            * 1.46.0   2020-04-27 [1]
##  stringi                1.5.3    2020-09-09 [1]
##  stringr              * 1.4.0    2019-02-10 [1]
##  SummarizedExperiment * 1.18.2   2020-07-09 [1]
##  testthat               3.0.0    2020-10-31 [1]
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##  tidyverse            * 1.3.0    2019-11-21 [1]
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##  xfun                   0.19     2020-10-30 [1]
##  xml2                   1.3.2    2020-04-23 [1]
##  XVector              * 0.28.0   2020-04-27 [1]
##  yaml                   2.2.1    2020-02-01 [1]
##  zlibbioc               1.34.0   2020-04-27 [1]
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##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  Bioconductor                                 
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  Bioconductor                                 
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  Bioconductor                                 
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  Bioconductor                                 
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  CRAN (R 4.0.3)                               
##  Bioconductor                                 
##  CRAN (R 4.0.3)                               
##  Bioconductor                                 
## 
## [1] /rugpfs/fs0/brc/scratch/mpaul/software/R-4.0.3/library